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Final

Cumulative Final Review (got 96%)

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Department
Biological Sciences
Course Code
BIOL 3090
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All

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BIOL 3090Fall 2012 FinalDimarioChapters 1 and 2 Dynamic CellChemical Foundations1 The model organisms Saccharomyces cerevisiayeast species that is studied to understand how cells divideCaenorhabditis elegansa roundwormDrosophilia metanogastera fruit fly studied to understand developmentZebrafish is a vertebrate with a true backbone It is used to study birth defects and cancerMice are used to study developmental biology Arabidosis thaliana is the only model organism used to study development in plantsViruses are used to study gene expression 2 Four aspects of the cell theory1 All living things are composed of cells and their products2 Cells are essentially alike in chemical constitution This is fundamental in biochemistry3 Ominis cellula e cellula All cells come from cells4 The activity of the organism as a whole is the sume of the activities and interactions of essentially independent cell units The cell is the closest thing to an autonomus biological unit that exists The cell is the fundamental unit of life3 Electronegativity to explaina polar and nonpolar covalent bondsElectrons are shared between atoms in covalent bonds Polar covalent bonds are hydrophilic The atoms making up the bond are significantly different in their electronegativity leading to unequal sharing of the electrons Nonpolar covalent bonds are hydrophobic Electrons are equally shared because there is no significant difference in the electronegativitiesb ionic bondsIonic bonds occur between atoms with opposite charges Cations have a positive charge Anions have a negative charge Salts can dissolve in water Increasing the concentrations of salts in a solution of biological molecules can weaken and even disrupt the ionic interactions holding the biomolecules togetherc hydrogen bondsA hydrogen atom is covalently bonded to a more electronegative atom oxygen such that the bond is polar then another electronegative atom nitrogen is attracted to the hydrogen by electrostatic interactions Nonlinear hydrogen bonds are weaker than linear ones Hydrogen bonds help stabilize protein structures because they are cumulative The more hydrogen bonds there are the more stable the structure is4 van der Waals and hydrophobic interactions Figs 210 and 211 are goodVan der Waals interaction are nonspecific interactions between two closely spaced atoms They are responsible for the cohesion between nonpolar molecules that cannot form hydrogen bonds or ionic interactions with other molecules Van der Waals interactions occur with both polar and nonpolar molecules If the atoms get too close then their outermost electron shells repel each otherHydrophobic interactions are a really important concept They deal with the energy required for inserting a nonpolar molecule into water Nonpolar molecules or functional groups CH cannot hydrogen bond with water so 3the molecule distorts the normal random structure of water Hydrophobic interactions are the principle driving mechanism for getting a protein to fold 1BIOL 3090Fall 2012 FinalDimarioproperly Nonpolar molecules or nonpolar portions of molecules tend to aggregate in water owning to a phenomenon called the hydrophobic effect 5 Amino acids Fig 214 nitrogenous bases Fig 217 glucose Fig 218 and phospholipids Fig 220All 20 amino acids are water soluble All are soluble in water due to carboxylic acid and amino groups on the alpha carbon Basic and acidic amino acid side R groups are charged in a living cell Cys Trp and Met are rare amino acids They only comprise 5 of amino acids in a protein Leu Ser Lys and Glu are the most abundant amino acids They comprise 32 of amino acids in a protein Hydrophobic amino acids are rich in methyl groups Proline is very rigid and creates a fixed kink in a protein chain limiting how a protein can fold in the region of proline residues Two cysteines can form disulfide bonds upon oxidation of their sulfhydryl groups The disulfide bonds then help maintain protein structure Proteins can be modified posttranslationally When lysine becomes acetylated is it not longer basic Thus it cannot interact with DNA anymore Phosphoserine is acidic rather than polarneutral like serine Acetyation is the most common ofrm of amino acid chemical modification affecting 80 of all proteins Nitrogenous bases fall into two categoriespurine and pyrimidines Adenine and guanine are both purines Adenine is the nitrogenous base found in ATP the major energy molecule in the cell The pyrimidines include uracil thymine and cytosine Uracil is only found in RNA Thymine is only found in DNA Glucose is an aldehyde surgar that exists in ring form within living cells Dglucose is the principle external source of energy for most cells in higher organisms The chair is the most stable configuration The pyranose form is the most abundant form of DglucosePhospholipids are the most important lipid The phospholipids are the necessary building blocks for biological membranes Phosphate is very hydrophilic The choline can change to other groups Phospholipids are ampiphathic both positively and negatively charged two sided 6 Reaction rates and chemical equilibriumAt chemical equilibrium the rates of the forward and reverse reactions are equal Concentrations of reactants and products might not be the same but they do not change at chemical equilibrium The ratio of products to reactants at equilibrium is the equilibrium constant K A catalyst will accelerate the eqforward and reverse reactions by the same factor so K does not change with a catalyst present The eqdissociation constant K reflects how tightly a protein can bind to DNA AvidinBiotin is the tightest dinteraction that we know of In a living cell some products never reach equilibrium because they are rapidly consumed When the rate of formation is equal to the rate of consumption the system is in a steady state2BIOL 3090Fall 2012 FinalDimario7 Definition of pH both the mathematical formula and what the formula meanspH is the concentration of H ions in solution In pure water H and OHare equimolar so OH7142and H are 1x10M each For any aqueous solution H x OH must equal 1x10 M If H goes up OH must go down If OH goes up H must go down pH is equal to the logH A pH below 7 is acidic A pH of 7 is neutral A pH above 7 is basic8 HendersonHasselbalch equation and what it means regarding biological buffers pKaWhat is the middle pKa of phosphoric acid and why is it important Fig 228The HendersonHasselbalch equation relates pH and K It explains eqhow buffers work and that living systems cells use buffers to maintain pH The pK of any acid is equal to the pH at which half the molecules are a dissociate and half are neutral It is unique for each weak acid Weak acidsfunction as buffers at pHs equal to their pKs At pH values more than one aunit above or below the pK the buffering capacity of weak acids and aweak bases declines rapidly 9 Positive and negative Gs Fig 229 ATP hydrolysis to drive coupled reactions forwardDA positive DG means you have to put energy into a reaction in order for the reaction go forward Therefore it is endothermic A negative DG means that energy was released from the reaction Therefore it is exothermic DG for a reaction is independent of the reaction rate Endothermic and exothermic reactions can be coupled together If the net gain is energy output the reactions will move forward Hydrolysis of ATP to PO and ADP is usually the exothermic reaction DG 4Dthat a cell couples to most endothermic reactions that have a positive G Chapter 3 Protein StructureFunction1 Know what atoms make up the peptide bond and how these atoms contribute to secondary structuresPeptide bonds are between the carbonyl group and the nitrogen with the hydrogen The carbonyl oxygen and aminde nitrogen that make up the peptide bond are both electronegative Peptide bonds form via dehydration They are planar bonds that behave like covalent double bonds There is no free rotation due to the carbonyl oxygen and the amide nitrogen R groups extend from the alphacarbon atoms of the amino acid There is free rotation about the covalent bonds to the alphacarbon within each amino acid The carbonyl oxygen is hydrogen bonded to an amide nitrogen four peptide bonds down stream to form alpha helices 2 Primary secondary Fig 34 and 35 tertiary Fig 37 and quaternary structures of proteinsPrimary structure is the linear sequence of amino acids Specific amino acid sequences contain all the intrinsic information on how a protein folds into its threedimensional structure Sickle cell anemia has one hemoglobin amino acid that isnt correct Therefore it doesnt fold correctlySecondary structure includes alpha helices beta strands reverse turns and random coils In an alpha helix the 3
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